[MINC-users] How to use rawtominc with multiple files

[Runa Parveen]

hi minc users,

I have sent this e-mail twice but nit getting any response. Please can you 
suggest me on those points.

Many thanks for your kind cooperation.

In some points, I am still struggling to proper use of this package.

1.   rawtominc -coronal -short -unsigned -scan_range \
    -xstep 1 -ystep 1 -zstep 1 \
    -xstart -10 -ystart -50 -zstart -50 \
     -mri data_pix_out.mnc 171 256 256 < data_pix_in.img
According to your suggestion, I have used the above command for the 
transfer image into minc format. But when I displayed the image in DISPLAY 
menu, I have seen negative value -16321.2 in some point shown between 
bottom .1000 and .2000 in the column of colour bar in the left hand side. 
Please let me know why this one is displaying.

2. also, when I check with mincheader command of the "data_pix_out.mnc" the
image-max = 65285, 65285, 65285, 65285...................
and
image_min = _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _,
     _, _, _, _, _, _, _, _,

Is there any information I missed to put in the rawtominc conversion 
command line?

3. In mincresample, what would be the position of centre of first voxel 
along each of the world dimensions? the command line I use:
mincresample data_pix_out.mnc data_pix_resample.mnc -transform 
data_pix_res.xfm -like average_305.mnc -step 1 1 1 -short -unsigned -range 
0 32767 -nearest_neighbour -nelements 171 256 256

I was trying to resample the input image with average_305.mnc in mritotal 
and mincresample command before using NU_CORRECT. Which would be the better 
solution for NU_CORRECT? directly use on input image or after transforming 
data in a model (average_305) and then use the intensity correction? Please 
give me suggestion in this regard.
THIS IS VERY URGENT :
4. I would like to transfer the *.minc image into *.raw after the 
correction to use my own algorithm run on the intensity corrected image. I 
was using the command
minctoraw -short -unsigned -normalize data_pix_out_nu.mnc > data_pix_out_nu.raw

The value in the raw file are varied from -32767 to 32767. My original 
input image is unsigned short, intensity voxel value min is zero and  max 
1700. I would like to return back the *.minc image after correction into 
the similar intensity level of input *.raw image and this is very urgent. 
Please give me the appropriate command line to transfer the image format.

My sincere thanks to you for your kind help.

Yours sincerely,

Runa

******************************************************************** 

* Runa Parveen                                                            **
* Medical Imaging Group                                               **
* Dept. of Medical Physics & Bioengineering                   **
* University College London                                            **
* 2nd Floor, New Malet Place Engineering Building           **
* Gower Street, off Torrington Place                                 **
* London WC1E 6JA                                                 **
* 
UK 
**
* Tel. +44 (0) 20 7679 0246 (Dept.)
          +44 (0) 7984 084 959 (mob.)                                  **
* Fax.+44 (0) 20 7679 0255 (Dept.)                                  **
* e-mail: runa at medphys.ucl.ac.uk                                  **
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